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Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

BIMA V3: an aligner customized for mate pair library sequencing.

Travis M Drucker¹, Sarah H Johnson¹, Stephen J Murphy¹

¹Department of Information Technology, MN 55905, Department of Molecular Medicine, Department of Laboratory Medicine and Pathology and Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.

Bioinformatics (Oxford, England)

|February 15, 2014

Summary

This summary is machine-generated.

We developed a new algorithm for mate pair sequencing analysis that significantly improves speed and accuracy. This method enhances the detection of genomic structural variants and chromosomal abnormalities, overcoming challenges in read mapping and alignment.

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Comparative Lesions Analysis Through a Targeted Sequencing Approach

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Published on: November 5, 2019

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Mate pair library sequencing is crucial for identifying genomic structural variants and chromosomal abnormalities.
Current next-generation sequencing alignment programs face challenges with mate-pair read mapping due to large insert sizes and library preparation artifacts.
Complexity arises from factors like biotin junction reads, contamination, chimeras, and breakpoints within reads.

Purpose of the Study:

To develop a faster and more accurate algorithm for mapping and aligning mate-pair sequencing reads.
To address the computational challenges associated with mate-pair data analysis.
To improve the efficiency and precision of genomic structural variant detection.

Main Methods:

Development of a novel algorithm specifically designed for mate-pair sequencing data.
Implementation of advanced computational techniques to handle large insert sizes and library artifacts.
Comparative analysis against popular next-generation sequencing alignment programs.

Main Results:

The new algorithm demonstrates up to 20 times greater speed compared to existing popular programs.
The algorithm achieves a 25% increase in accuracy for mate-pair read mapping and alignment.
Successfully addresses complexities introduced by library preparation and structural variant breakpoints.

Conclusions:

The developed algorithm offers a significant advancement in mate-pair sequencing analysis.
This method provides a more efficient and accurate approach for detecting genomic structural variants and chromosomal abnormalities.
The enhanced performance has implications for various genomic research and clinical applications.